Anomeric effect in pyranose-ring derivatives containing carbon,silicon, and germanium as anomeric centers: an ab initio systematic study

Structural Chemistry - We have performed a systematic conformational analysis focused on the evaluation of the anomeric effect (AE) in a series of pyranose derivatives containing carbon, silicon,...     

Synthesis and structural study of ethylmethylsilanediol by quantum chemical calculations and IR and Raman spectroscopies

The intrinsic instability of small alkylsilanediols and their propensity toward self-condensation have been the main determiners of the scarce number of experimental works dealing with their synthesis and vibrational characterization. This is the case of the title compound, ethylmethylsilanediol (EMSD), which preparation and purification is, to the best of our knowledge, firstly reported in the present work. Hence, we also report the first records of the IR and Raman spectra of the molecule that have been thoroughly analyzed and completely assigned with the support of DFT calculations. Further, as a previous step of the vibrational assignment, we accomplished a thorough conformational analysis that allowed indentifying five conformations that represent minima on the potential energy surface (PES) of the molecule, depending on the different arrangement that both, the alkyl side chain and the –OH groups, can adopt. Finally, natural bond orbital (NBO) calculations were implemented to justify the stability order and the calculated geometries for the set of conformers in terms of the stabilization derived from the anomeric effect.     

A New Derivation of the Quantum Navier–Stokes Equations in the Wigner–Fokker–Planck Approach

A quantum Navier–Stokes system for the particle, momentum, and energy densities is formally derived from the Wigner–Fokker–Planck equation using a moment method. The viscosity term depends on the particle density with a shear viscosity coefficient which equals the quantum diffusion coefficient of the Fokker–Planck collision operator. The main idea of the derivation is the use of a so-called osmotic momentum operator, which is the sum of the phase-space momentum and the gradient operator. In this way, a Chapman–Enskog expansion of the Wigner function, which typically leads to viscous approximations, is avoided. Moreover, we show that the osmotic momentum emerges from local gauge theory.     

DFT‐Aided Vibrational Circular Dichroism Spectroscopy Study of (−)‐S‐cotinine

The implementation of a strategy comprising the use of vibrational circular dichroism spectroscopy and DFT calculations allows determination of the solution‐state conformational distribution in (?)‐S‐cotinine, giving further proof of the extra conformer‐discriminating potential of this experimental technique, which may offer unique molecular fingerprints of subtly dissimilar molecular conformers of chiral samples. Natural bond orbital electronic structure calculations of the rotational barrier height between the two main conformers of the species indicate that hyperconjugative effects are the key force governing the conformational equilibrium. The negligible effect of the solvent’s polarity over both structure and conformational energy profile supports this result.     

Effect of substituents and hydrogen bonding on barrier heights in dehydration reactions of carbon and silicon geminal diols

Activation barrier heights for the dehydration reaction of geminal carbinols and silanediols R'R″X(OH)(2) (X = C, Si) were estimated at the B3LYP and MP2 levels of theory employing Dunning's correlation-consistent triple-zeta basis sets. It was shown that the barrier height for carbon derivatives steadily decreases upon substitution by R groups, usually termed as electron-donating, such as alkyl and amino groups. Substitution by electron-withdrawing groups leads, however, only to small changes in barrier heights compared to that of methanediol. A similar tendency was also found for silicon derivatives, but high activation barriers of this reaction remain even for amino group substituted silanediols. Introduction of additional water molecules into the reactive space of carbinol dehydration drastically reduces barrier heights and brings the transition state energy for methanediol close to the experimental value. The difference between dehydration barrier heights for both methanediol and carbinols with electron-rich substituents becomes well-defined for dimeric species. The higher acidity of the hydroxyl group protons in molecules containing halogens and C==O groups brings about a noticeable growth in the dehydration barrier heights of these compounds. This difference in barrier heights for oligomeric species may be the reason for the stability of carbinols with electron-rich substituents.     

The vibrational spectra of (CH3)3SiX (S=H, F, Br) molecules, revisited Transferable scale factor sets for methylsilane derivatives

The joint experimental and theoretical study of the vibrational spectra of the molecular series (CH3)3SiX (with X=H, F and Br) is carried out. Data from newly recorded IR and Raman spectra for the bromo derivative, experimental data obtained previously for the remaining species, DFT theoretical calculations and the use of the SQMFF procedure have allowed us to propose common patterns and to unify criteria in their assignment. In addition, two sets of averaged scale factors for the B3LYP force field obtained with two different basis sets (6-31G* and DZP+diff) have been proposed for the common bulky moiety of that molecular series. These parameters were used successfully in order to reproduce the frequency of the bands assigned to the (CH3)3Si- group in the vibrational spectra of the corresponding silanolic and methoxy derivatives, i.e., trimethylsilanol and methoxytrimethylsilane, proving their transferability.     

Structure and vibrational spectra of Ti(IV) hydroxides and their clusters with expanded titanium coordination. DFT study

Equilibrium structures of H(4-n)Ti(OH)n (n = 2-4) molecules and the Ti(OH)4 dimer and trimers were optimized at the B3LYP level of theory. Theoretical vibrational frequencies of TiO stretching modes obtained with several basis sets were compared with the existing experimental frequencies of these vibrations, and the 6-31+G(d) set was chosen for cluster calculations. Only one energy minimum was found for the [Ti(OH)4](2) dimer, but two isomers without symmetry elements stabilized by internal hydrogen bonds and two isomers, belonging to C(s) and C(i) point groups, with free OH groups were found as minima at the [Ti(OH)4](3) potential energy surface. The structure with the linear arrangement of hexacoordinated titanium atoms in the Ti3O12 skeleton may be proposed for trimeric species observed in liquid titanium alkoxides as the only structure satisfying experimental spectroscopic evidence about the presence of center of inversion in these species. Frequency changes of TiO4 modes which accompany the oligomer formation are predicted and discussed.     

Mechanism of the Catalytic Activity of Nucleophiles in the Stepwise Hydrolysis and Condensation Reactions of Tetramethoxysilane

Active ingredients : A model for the simplest hydrolysis reaction is applied to all stages of stepwise hydrolysis and condensation taking place during a sol–gel process. The picture shows the molecular structures of the transition states of the ammonia‐ (left) and OH^?‐promoted (right) condensation reactions of two Si(OH)₄ molecules, including an additional water molecule.

     

Multi-start and path relinking methods to deal with multiobjective knapsack problems

This paper deals with a multiobjective combinatorial optimization problem called Extended Knapsack Problem. By applying multi-start search and path relinking we rapidly guide the search toward the most balanced zone of the Pareto-optimal front. The Pareto relation is applied in order to designate a subset of the best generated solutions to be the current efficient set of solutions. The max-min criterion with the Hamming distance is used as a measure of dissimilarity in order to find diverse solutions to be combined. The performance of our approach is compared with several state-of-the-art MOEAs for a suite test problems taken from the literature.     

Interaction models of the Si(OH)2 functionality with Zn2+ cation in simplified biological environments: a DFT study

We report a DFT study (M06L/cc-pVDZ) of the interactions between the Si(OH)₂ group in three simplified gem-silanediols [i.e., N-[dihydroxy(methyl)silyl] methyl}formamide (DHSF), 3-[dihydroxy (methyl) silyl] propanamide (DHSP), and 3,3′-(dihydroxysilanediyl)dipropanamide (DHSDP)], which have a similar structure to silanediol-based inhibitors of metalloproteases, and simplified active site models: [Zn(Imdz)₃–OH₂]²⁺ and [Zn(Imdz)₂R–OH₂]²⁺, where R can be a formaldehyde, an acetone, or an acetic acid molecule. These models partly resemble the structure of the first coordination sphere of some metalloproteases (e.g., angiotensin I converting enzyme and thermolysin). Different types of bonding patterns were found for the systems into study. The three related silanediols may coordinate with the zinc dication in monodentate, pseudo-bidentate, and pseudo-tridentate way. Pseudo-bidentate interaction was reported to be that corresponding to the silanediol transition-state-analog of the thermolysin enzyme as confirmed by the X-ray structural study (Juers et al., Biochemistry 44:16524–16528, 2005). The binding ability of the mentioned silanediols was determined as the energy of the water displacement reaction for the mentioned active sites models in gas phase and in water solution (PCM model). The calculated binding energies point out to the higher strength of the pseudo-bidentate Zn²⁺–MBG interaction. Moreover, DHSDP ligand is calculated to be the strongest MBG for Zn²⁺ in both active sites models. NBO population analysis and the AIM methodology were implemented as a tool for evaluating electronic structure of the complexes. The results obtained may point out to the fact that the higher the electronic delocalization around the metal center is, the stronger the interaction between the MBG and the active site, bringing about a higher binding energy.